You'll see that this pdf is also a password protected pdf, but you CAN extract its cover.

Look at the attached screenshots which show permissions for the conflictive Canon.pdf and for this document. (They're in Spanish but I suppose you can easily follow them. You can also directly test both files in your own installation of Adobe Reader XI).

So I can see two possible scenarios:
+Everything is working as expected. The newest flavour of the Acrobat protection actually prevents and will always prevent Calibre from getting the cover.
+Calibre pdf cover extractor is OUTDATED. I mean there's nothing in the pdf which blocks the Cover extraction but an old version of the Calibre built-in pdf renderer which cannot handle that new Adobe X procedure or 256bit AES key. A "simple" (between quotes) update of this part of the software would allow the cover extraction without further problems.